Statistical Applications in Genetics and Molecular Biology

2002 - 2012

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Volume 11, issue 5, 2012

DNA Pooling and Statistical Tests for the Detection of Single Nucleotide Polymorphisms pp. 1

David M. Ramsey and Andreas Futschik

Comparison of Targeted Maximum Likelihood and Shrinkage Estimators of Parameters in Gene Networks pp. 2

Geert Geeven, Mark J. van der Laan and Mathisca C.M. de Gunst

A PAUC-based Estimation Technique for Disease Classification and Biomarker Selection pp. 3

Matthias Schmid, Torsten Hothorn, Friedemann Krause and Christina Rabe

Estimators of the local false discovery rate designed for small numbers of tests pp. 4

Marta Padilla and David R. Bickel

Genotype Copy Number Variations using Gaussian Mixture Models: Theory and Algorithms pp. 5

Chang-Yun Lin, Yungtai Lo and Kenny Q. Ye

Analyzing Genetic Association Studies with an Extended Propensity Score Approach pp. 6

Huaqing Zhao, Timothy R. Rebbeck and Nandita Mitra

Empirical Bayesian Selection of Hypothesis Testing Procedures for Analysis of Sequence Count Expression Data pp. 7

Stanley B. Pounds, Cuilan L. Gao and Hui Zhang

Detecting Differential Expression in RNA-sequence Data Using Quasi-likelihood with Shrunken Dispersion Estimates pp. 8

Steven P. Lund, Dan Nettleton, Davis J. McCarthy and Gordon K. Smyth

Variational Bayes Procedure for Effective Classification of Tumor Type with Microarray Gene Expression Data pp. 9

Takeshi Hayashi

Incorporating Genomic Annotation into a Hidden Markov Model for DNA Methylation Tiling Array Data pp. 10

Gayla R. Olbricht, Bruce A. Craig and Rebecca W. Doerge

ExactDAS: An Exact Test Procedure for the Detection of Differential Alternative Splicing in Microarray Experiments pp. 11

Tristan Mary-Huard, Florence Jaffrezic and Stéphane Robin

Large-scale Parentage Inference with SNPs: an Efficient Algorithm for Statistical Confidence of Parent Pair Allocations pp. 12

Eric C. Anderson

Volume 11, issue 4, 2012

Computing Posterior Probabilities for Score-based Alignments Using ppALIGN pp. 1

Stefan Wolfsheimer, Alexander Hartmann, Ralf Rabus and Gregory Nuel

QTL Mapping Using a Memetic Algorithm with Modifications of BIC as Fitness Function pp. 2

Florian Frommlet, Ivana Ljubic, Helga Björk Arnardóttir and Malgorzata Bogdan

A Bayesian autoregressive three-state hidden Markov model for identifying switching monotonic regimes in Microarray time course data pp. 3

Alessio Farcomeni and Serena Arima

Performance of MAX Test and Degree of Dominance Index in Predicting the Mode of Inheritance pp. 4

Elias Zintzaras and Mauro Santos

A Novel and Fast Normalization Method for High-Density Arrays pp. 5

Maarten van Iterson, Floor A.M. Duijkers, Jules P.P. Meijerink, Pieter Admiraal, Gert-Jan B. van Ommen, Judith M. Boer, Max M. van Noesel and Renee X. Menezes

An Integrated Hierarchical Bayesian Model for Multivariate eQTL Mapping pp. 6

Marie Pier Scott-Boyer, Gregory C. Imholte, Arafat Tayeb, Aurelie Labbe, Christian F. Deschepper and Raphael Gottardo

A Non-Homogeneous Dynamic Bayesian Network with Sequentially Coupled Interaction Parameters for Applications in Systems and Synthetic Biology pp. 7

Marco Grzegorczyk and Dirk Husmeier

Correction for Founder Effects in Host-Viral Association Studies via Principal Components pp. 8

Karyn L. Reeves, Elizabeth J. McKinnon and Ian R. James

Testing clonality of three and more tumors using their loss of heterozygosity profiles pp. 9

Irina Ostrovnaya

Estimating the Number of One-step Beneficial Mutations pp. 10

Andrzej J. Wojtowicz, Craig R. Miller and Paul Joyce

Incorporating the Empirical Null Hypothesis into the Benjamini-Hochberg Procedure pp. 11

Debashis Ghosh

How to analyze many contingency tables simultaneously in genetic association studies pp. 12

Thorsten Dickhaus, Klaus Straßburger, Daniel Schunk, Carlos Morcillo-Suarez, Thomas Illig and Arcadi Navarro

Cluster-Localized Sparse Logistic Regression for SNP Data pp. 13

Harald Binder, Tina Müller, Holger Schwender, Klaus Golka, Michael Steffens, Jan G. Hengstler, Katja Ickstadt and Martin Schumacher

Hessian Calculation for Phylogenetic Likelihood based on the Pruning Algorithm and its Applications pp. 14

Toby Kenney and Hong Gu

A New Explained-Variance Based Genetic Risk Score for Predictive Modeling of Disease Risk pp. 15

Ronglin Che and Alison A. Motsinger-Reif

Volume 11, issue 3, 2012

A New Approach for the Joint Analysis of Multiple Chip-Seq Libraries with Application to Histone Modification pp. 1

John P. Ferguson, Judy H. Cho and Hongyu Zhao

Sample Size Calculations for Designing Clinical Proteomic Profiling Studies Using Mass Spectrometry pp. 2

Stephen O. Nyangoma, Stuart I. Collins, Douglas G. Altman, Philip Johnson and Lucinda J. Billingham

Graph Selection with GGMselect pp. 3

Christophe Giraud, Sylvie Huet and Nicolas Verzelen

Non-Iterative, Regression-Based Estimation of Haplotype Associations with Censored Survival Outcomes pp. 4

Benjamin French, Thomas Lumley, Thomas P. Cappola and Nandita Mitra

Detection of Differentially Expressed Gene Sets in a Partially Paired Microarray Data Set pp. 5

Johan Lim, Jayoun Kim, Sang-cheol Kim, Donghyeon Yu, Kyunga Kim and Byung Soo Kim

GENOVA: Gene Overlap Analysis of GWAS Results pp. 6

Clara S. Tang and Manuel A. R. Ferreira

Empirical Bayes Interval Estimates that are Conditionally Equal to Unadjusted Confidence Intervals or to Default Prior Credibility Intervals pp. 7

David R. Bickel

Combining Multiple Laser Scans of Spotted Microarrays by Means of a Two-Way ANOVA Model pp. 8

Jérôme Ambroise, Bertrand Bearzatto, Annie Robert, Benoit Macq and Jean-Luc Gala

Normalization, bias correction, and peak calling for ChIP-seq pp. 9

Aaron Diaz, Kiyoub Park, Daniel A. Lim and Jun S. Song

The practical effect of batch on genomic prediction pp. 10

Hilary S. Parker and Jeffrey T. Leek

Hierarchical Bayes Model for Predicting Effectiveness of HIV Combination Therapies pp. 11

Jasmina Bogojeska and Thomas Lengauer

Borrowing Information Across Genes and Experiments for Improved Error Variance Estimation in Microarray Data Analysis pp. 12

Tieming Ji, Peng Liu and Dan Nettleton

Detecting Sample Misidentifications in Genetic Association Studies pp. 13

Claus T. Ekstrøm and Bjarke Feenstra

The Beta-Binomial SGoF method for multiple dependent tests pp. 14

Jacobo de Uña-Alvarez

Exploring Multicollinearity Using a Random Matrix Theory Approach pp. 15

Kristen Feher, James Whelan and Samuel Müller

Volume 11, issue 2, 2012

Special Issue on Computational Statistical Methods for Genomics and Systems Biology pp. 1

Aurélie Labbe and Sandrine Dudoit

A Generalized Hidden Markov Model for Determining Sequence-based Predictors of Nucleosome Positioning pp. 2

Carlee Moser and Mayetri Gupta

Gene Filtering in the Analysis of Illumina Microarray Experiments pp. 3

Anyiawung Chiara Forcheh, Geert Verbeke, Adetayo Kasim, Dan Lin, Ziv Shkedy, Willem Talloen, Hinrich WH Göhlmann and Lieven Clement

Principal Components of Heritability for High Dimension Quantitative Traits and General Pedigrees pp. 4

Karim Oualkacha, Aurelie Labbe, Antonio Ciampi, Marc-Andre Roy and Michel Maziade

Bayesian Sparsity-Path-Analysis of Genetic Association Signal using Generalized t Priors pp. 5

Anthony Lee, Francois Caron, Arnaud Doucet and Chris Holmes

A Family-Based Probabilistic Method for Capturing De Novo Mutations from High-Throughput Short-Read Sequencing Data pp. 6

Reed A. Cartwright, Julie Hussin, Jonathan E. M. Keebler, Eric A. Stone and Philip Awadalla

Adjusting for Spurious Gene-by-Environment Interaction Using Case-Parent Triads pp. 7

Ji-Hyung Shin, Claire Infante-Rivard, Jinko Graham and Brad McNeney

Querying Genomic Databases: Refining the Connectivity Map pp. 8

Mark R. Segal, Hao Xiong, Henrik Bengtsson, Richard Bourgon and Robert Gentleman

A Model-Based Analysis to Infer the Functional Content of a Gene List pp. 9

Michael A. Newton, Qiuling He and Christina Kendziorski

Candidate Pathway Based Analysis for Cleft Lip with or without Cleft Palate pp. 10

Tian-Xiao Zhang, Terri H. Beaty and Ingo Ruczinski

Improving Pedigree-based Linkage Analysis by Estimating Coancestry Among Families pp. 11

Chris Glazner and Elizabeth Alison Thompson

Volume 11, issue 1, 2012

Improving Hidden Markov Models for Classification of Human Immunodeficiency Virus-1 Subtypes through Linear Classifier Learning pp. 1

Ingo Bulla, Anne-Kathrin Schultz and Peter Meinicke

Transcriptional Network Inference from Functional Similarity and Expression Data: A Global Supervised Approach pp. 2

Jérôme Ambroise, Annie Robert, Benoit Macq and Jean-Luc Gala

Alignment-free Sequence Comparison for Biologically Realistic Sequences of Moderate Length pp. 3

Conrad J. Burden, Junmei Jing and Susan R. Wilson

Fast Wavelet Based Functional Models for Transcriptome Analysis with Tiling Arrays pp. 4

Lieven Clement, Kristof De Beuf, Olivier Thas, Marnik Vuylsteke, Rafael A. Irizarry and Ciprian M. Crainiceanu

A Context Dependent Pair Hidden Markov Model for Statistical Alignment pp. 5

Ana Arribas-Gil and Catherine Matias

MicroRNA Transcription Start Site Prediction with Multi-objective Feature Selection pp. 6

Malay Bhattacharyya, Lars Feuerbach, Tapas Bhadra, Thomas Lengauer and Sanghamitra Bandyopadhyay

Fast Identification of Biological Pathways Associated with a Quantitative Trait Using Group Lasso with Overlaps pp. 7

Matt Silver, Giovanni Montana and Alzheimer's Disease Neuroimaging Initiative

A Mixture-Model Approach for Parallel Testing for Unequal Variances pp. 8

Haim Y. Bar, James G. Booth and Martin T. Wells

Stopping-Time Resampling and Population Genetic Inference under Coalescent Models pp. 9

Paul A. Jenkins

Optimality Criteria for the Design of 2-Color Microarray Studies pp. 10

Kathleen F. Kerr

The Inheritance Procedure: Multiple Testing of Tree-structured Hypotheses pp. 11

Jelle J. Goeman and Livio Finos